Examples with BaseStudyTable org.obiba.mica.core.domain.BaseStudyTable used on opensource projects

Example 1 with BaseStudyTable

use of org.obiba.mica.core.domain.BaseStudyTable in project mica2 by obiba.

the class PublishedDataschemaDatasetVariableResource method getVariableAggregations.

@GET
@Path("/aggregation")
@Timed
public Mica.DatasetVariableAggregationsDto getVariableAggregations() {
    ImmutableList.Builder<Mica.DatasetVariableAggregationDto> builder = ImmutableList.builder();
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    Mica.DatasetVariableAggregationsDto.Builder aggDto = Mica.DatasetVariableAggregationsDto.newBuilder();
    List<Future<Math.SummaryStatisticsDto>> results = Lists.newArrayList();
    dataset.getBaseStudyTables().forEach(table -> results.add(helper.getVariableFacet(dataset, variableName, table)));
    for (int i = 0; i < dataset.getBaseStudyTables().size(); i++) {
        BaseStudyTable opalTable = dataset.getBaseStudyTables().get(i);
        Future<Math.SummaryStatisticsDto> futureResult = results.get(i);
        try {
            builder.add(dtos.asDto(opalTable, futureResult.get()).build());
        } catch (Exception e) {
            log.warn("Unable to retrieve statistics: " + e.getMessage(), e);
            builder.add(dtos.asDto(opalTable, null).build());
        }
    }
    List<Mica.DatasetVariableAggregationDto> aggsDto = builder.build();
    Mica.DatasetVariableAggregationDto allAggDto = CombinedStatistics.mergeAggregations(aggsDto);
    aggDto.setN(allAggDto.getN());
    aggDto.setTotal(allAggDto.getTotal());
    if (allAggDto.hasStatistics())
        aggDto.setStatistics(allAggDto.getStatistics());
    aggDto.addAllFrequencies(allAggDto.getFrequenciesList());
    aggDto.addAllAggregations(aggsDto);
    return aggDto.build();
}

Example 2 with BaseStudyTable

use of org.obiba.mica.core.domain.BaseStudyTable in project mica2 by obiba.

the class DatasetController method dataset.

@GetMapping("/dataset/{id:.+}")
public ModelAndView dataset(@PathVariable String id, @RequestParam(value = "draft", required = false) String shareKey) {
    Map<String, Object> params = newParameters();
    Dataset dataset = getDataset(id, shareKey);
    params.put("dataset", dataset);
    params.put("type", (dataset instanceof StudyDataset) ? "Collected" : "Harmonized");
    params.put("draft", !Strings.isNullOrEmpty(shareKey));
    if (dataset instanceof StudyDataset) {
        addStudyTableParameters(params, ((StudyDataset) dataset).getStudyTable());
    } else {
        HarmonizationDataset harmoDataset = (HarmonizationDataset) dataset;
        addHarmonizationTableParameters(params, harmoDataset.getHarmonizationTable());
        Map<String, BaseStudy> allStudies = Maps.newHashMap();
        List<BaseStudyTable> allTables = Lists.newArrayList();
        List<Map<String, Object>> studyTables = Lists.newArrayList();
        List<String> ids = Lists.newArrayList();
        for (StudyTable sTable : harmoDataset.getStudyTables()) {
            Map<String, Object> p = new HashMap<>();
            if (addStudyTableParameters(p, sTable, ids))
                allTables.add(sTable);
            if (!p.isEmpty()) {
                studyTables.add(p);
                allStudies.put(sTable.getStudyId(), (BaseStudy) p.get("study"));
            }
        }
        params.put("studyTables", studyTables);
        List<Map<String, Object>> harmonizationTables = Lists.newArrayList();
        ids.clear();
        for (HarmonizationStudyTable hTable : harmoDataset.getHarmonizationTables()) {
            Map<String, Object> p = new HashMap<>();
            if (addHarmonizationTableParameters(p, hTable, ids))
                allTables.add(hTable);
            if (!p.isEmpty()) {
                harmonizationTables.add(p);
                allStudies.put(hTable.getStudyId(), (BaseStudy) p.get("study"));
            }
        }
        params.put("harmonizationTables", harmonizationTables);
        params.put("allTables", allTables);
        params.put("allStudies", allStudies);
    }
    params.put("showDatasetContingencyLink", showDatasetContingencyLink());
    return new ModelAndView("dataset", params);
}

Example 3 with BaseStudyTable

use of org.obiba.mica.core.domain.BaseStudyTable in project mica2 by obiba.

the class PublishedDataschemaDatasetVariableResource method getVariableAggregations.

@GET
@Path("/aggregation")
@Timed
public Mica.DatasetVariableAggregationsDto getVariableAggregations(@QueryParam("study") @DefaultValue("true") boolean withStudySummary) {
    checkDatasetAccess();
    checkVariableSummaryAccess();
    ImmutableList.Builder<Mica.DatasetVariableAggregationDto> builder = ImmutableList.builder();
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    Mica.DatasetVariableAggregationsDto.Builder aggDto = Mica.DatasetVariableAggregationsDto.newBuilder();
    List<Future<Math.SummaryStatisticsDto>> results = Lists.newArrayList();
    dataset.getBaseStudyTables().forEach(table -> results.add(helper.getVariableFacet(dataset, variableName, table)));
    for (int i = 0; i < dataset.getBaseStudyTables().size(); i++) {
        BaseStudyTable opalTable = dataset.getBaseStudyTables().get(i);
        Future<Math.SummaryStatisticsDto> futureResult = results.get(i);
        try {
            builder.add(dtos.asDto(opalTable, futureResult.get(), withStudySummary).build());
        } catch (Exception e) {
            log.warn("Unable to retrieve statistics: " + e.getMessage(), e);
            builder.add(dtos.asDto(opalTable, null, withStudySummary).build());
        }
    }
    List<Mica.DatasetVariableAggregationDto> aggsDto = builder.build();
    Mica.DatasetVariableAggregationDto allAggDto = CombinedStatistics.mergeAggregations(aggsDto);
    aggDto.setN(allAggDto.getN());
    aggDto.setTotal(allAggDto.getTotal());
    if (allAggDto.hasStatistics())
        aggDto.setStatistics(allAggDto.getStatistics());
    aggDto.addAllFrequencies(allAggDto.getFrequenciesList());
    aggDto.addAllAggregations(aggsDto);
    return aggDto.build();
}

Example 4 with BaseStudyTable

use of org.obiba.mica.core.domain.BaseStudyTable in project mica2 by obiba.

the class PublishedDataschemaDatasetVariableResource method getDatasetVariableContingenciesDto.

// 
// Private methods
// 
private Mica.DatasetVariableContingenciesDto getDatasetVariableContingenciesDto(DatasetVariable var, DatasetVariable crossVar) {
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    Mica.DatasetVariableContingenciesDto.Builder crossDto = Mica.DatasetVariableContingenciesDto.newBuilder();
    List<Future<Search.QueryResultDto>> results = Lists.newArrayList();
    dataset.getBaseStudyTables().forEach(table -> results.add(helper.getContingencyTable(dataset, var, crossVar, table)));
    Multimap<String, Mica.DatasetVariableAggregationDto> termAggregations = LinkedListMultimap.create();
    for (int i = 0; i < dataset.getBaseStudyTables().size(); i++) {
        BaseStudyTable opalTable = dataset.getBaseStudyTables().get(i);
        Future<Search.QueryResultDto> futureResult = results.get(i);
        try {
            Mica.DatasetVariableContingencyDto studyTableCrossDto = dtos.asContingencyDto(opalTable, var, crossVar, futureResult.get()).build();
            termAggregations.put(null, studyTableCrossDto.getAll());
            studyTableCrossDto.getAggregationsList().forEach(termAggDto -> termAggregations.put(termAggDto.getTerm(), termAggDto));
            crossDto.addContingencies(studyTableCrossDto);
        } catch (Exception e) {
            log.warn("Unable to retrieve contingency table: " + e.getMessage(), e);
            crossDto.addContingencies(dtos.asContingencyDto(opalTable, var, crossVar, null));
        }
    }
    // Merge aggregations by term (=variable category) + all terms aggregation.
    Mica.DatasetVariableContingencyDto.Builder allContingencies = Mica.DatasetVariableContingencyDto.newBuilder();
    termAggregations.asMap().entrySet().forEach(entry -> {
        Mica.DatasetVariableAggregationDto merged = CombinedStatistics.mergeAggregations(entry.getValue());
        if (entry.getKey() == null) {
            allContingencies.setAll(merged);
        } else {
            allContingencies.addAggregations(merged);
        }
    });
    crossDto.setAll(allContingencies);
    return crossDto.build();
}

Example 5 with BaseStudyTable

use of org.obiba.mica.core.domain.BaseStudyTable in project mica2 by obiba.

the class PublishedHarmonizedDatasetVariableResource method getVariableAggregations.

@GET
@Path("/aggregation")
@Timed
public Mica.DatasetVariableAggregationDto getVariableAggregations(@QueryParam("study") @DefaultValue("true") boolean withStudySummary) {
    checkDatasetAccess();
    checkVariableSummaryAccess();
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    for (BaseStudyTable opalTable : dataset.getBaseStudyTables()) {
        String opalTableId = studyId;
        if (opalTable.isFor(opalTableId, project, table)) {
            try {
                return dtos.asDto(opalTable, datasetService.getVariableSummary(dataset, variableName, studyId, project, table).getWrappedDto(), withStudySummary).build();
            } catch (Exception e) {
                log.warn("Unable to retrieve statistics: " + e.getMessage(), e);
                return dtos.asDto(opalTable, null, withStudySummary).build();
            }
        }
    }
    throw new NoSuchValueTableException(project, table);
}